Java (JAR)

Installing Java JAR

Google the package: GATK

In this case: need to create an account with the Broad institute

Download the GATK 3.6 to your computer

Upload the zipped file to your /home directory on the cluster

Unzip the files on your home directory: /home/XXX/gatk

Create the necessary environment variable (see Module section), .e.g. export GATK="/home/XXX/gatk/GenomeAnalysisTK.jar

Run your binaries on the cluster

java -jar /home/XXX/gatk/GenomeAnalysisTK.jar -h

java -jar $GATK -h (optional - if this is setup in .bashrc file)

java -jar /home/XXX/gatk/GenomeAnalysisTK.jar -T CountReads -R exampleFASTA.fasta -I exampleBAM.bam